Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals

BMC Genomics

Research Article

Adrian Carr¹  Gos Micklem¹  Till Bayer²  Manuel Aranda²  Christian R Voolstra²  Sebastian Baumgarten²  Yi Jin Liew³ 

[1] Cambridge Systems Biology Centre & Department of Genetics, University of Cambridge, Cambridge, UK;Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, 23955, Thuwal, Saudi Arabia;Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, 23955, Thuwal, Saudi Arabia;Cambridge Systems Biology Centre & Department of Genetics, University of Cambridge, Cambridge, UK;

关键词: Symbiodinium;    Dinoflagellates;    Scleractinian corals;    Symbiont;    Coral reef;    Small RNA (smRNA);    microRNA (miRNA);    Small interfering RNA (siRNA);    mRNA;    Expression profiling;    RNAseq;   

DOI  :  10.1186/1471-2164-14-704

 received in 2013-05-28, accepted in 2013-09-25,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundAnimal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous smRNAs and potential gene targets in dinoflagellates, we conducted smRNA and mRNA expression profiling over 9 experimental treatments of cultures from Symbiodinium microadriaticum, a photosynthetic symbiont of scleractinian corals.ResultsWe identified a set of 21 novel smRNAs that share stringent key features with functional microRNAs from other model organisms. smRNAs were predicted independently over all 9 treatments and their putative gene targets were identified. We found 1,720 animal-like target sites in the 3'UTRs of 12,858 mRNAs and 19 plant-like target sites in 51,917 genes. We assembled a transcriptome of 58,649 genes and determined differentially expressed genes (DEGs) between treatments. Heat stress was found to produce a much larger number of DEGs than other treatments that yielded only few DEGs. Analysis of DEGs also revealed that minicircle-encoded photosynthesis proteins seem to be common targets of transcriptional regulation. Furthermore, we identified the core RNAi protein machinery in Symbiodinium.ConclusionsIntegration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. protein modification, signaling, gene expression, and response to DNA damage. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.

【 授权许可】

Unknown   
© Baumgarten et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.